LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# SRD diffusion demo - dimer particles

units           lj
atom_style      sphere
atom_modify     map array first big
dimension       2

# read in clusters of rigid bodies

fix             molprop all property/atom mol ghost yes
read_data       data.dimer fix molprop NULL Molecules
Reading data file ...
  orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  200 atoms
  read_data CPU = 0.001 seconds

set             type 1 mass 1.0
Setting atom values ...
  200 settings made for mass
group           big type 1
200 atoms in group big
velocity        big create 1.44 87287 loop geom

# equilibrate big particles

pair_style      soft 1.12
pair_coeff      1 1 0.0
pair_coeff      2 2 0.0 0.0
pair_coeff      1 2 0.0 0.0

variable        prefactor equal ramp(0,60)
fix             soft all adapt 1 pair soft a * * v_prefactor

fix             1 big rigid molecule
  100 rigid bodies with 200 atoms
fix             2 all enforce2d

#dump           1 all atom 10 dump.dimer.equil

thermo          100
run             1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.42
  ghost atom cutoff = 1.42
  binsize = 0.71, bins = 27 27 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair soft, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.557 | 5.557 | 5.557 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   3.4028231      0              0              0.83369167    -0.55065517   
       100   9.5167872      2.392105       0              4.7237178      2.8319556    
       200   13.564465      3.0352634      0              6.3585572      3.6388732    
       300   13.133051      4.3835112      0              7.6011086      4.060051     
       400   14.576837      5.5141059      0              9.0854309      4.422762     
       500   15.227825      6.6472106      0              10.378028      4.8598912    
       600   16.93219       7.454865       0              11.603251      5.2908894    
       700   16.573769      8.7323442      0              12.792918      5.3544684    
       800   17.482599      9.7221047      0              14.005341      5.6200973    
       900   18.548144      10.739353      0              15.283649      4.7817995    
      1000   18.068079      12.058417      0              16.485096      6.5773091    
Loop time of 0.0511113 on 1 procs for 1000 steps with 200 atoms

Performance: 8452141.519 tau/day, 19565.142 timesteps/s, 3.913 Matom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0095507  | 0.0095507  | 0.0095507  |   0.0 | 18.69
Neigh   | 0.0042239  | 0.0042239  | 0.0042239  |   0.0 |  8.26
Comm    | 0.002203   | 0.002203   | 0.002203   |   0.0 |  4.31
Output  | 8.8531e-05 | 8.8531e-05 | 8.8531e-05 |   0.0 |  0.17
Modify  | 0.03336    | 0.03336    | 0.03336    |   0.0 | 65.27
Other   |            | 0.001685   |            |       |  3.30

Nlocal:            200 ave         200 max         200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             64 ave          64 max          64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:            275 ave         275 max         275 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 275
Ave neighs/atom = 1.375
Neighbor list builds = 193
Dangerous builds = 0

#undump         1
unfix           soft
unfix           1
unfix           2

# add small particles as hi density lattice

region          plane block INF INF INF INF -0.001 0.001 units box
lattice         sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms    2 region plane
Created 29929 atoms
  using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
  create_atoms CPU = 0.007 seconds

set             type 2 mass 0.1
Setting atom values ...
  29929 settings made for mass
group           small type 2
29929 atoms in group small
velocity        small create 1.0 593849 loop geom

# delete overlaps
# must set 1-2 cutoff to non-zero value

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0
pair_coeff      2 2 0.0 1.0 0.0
pair_coeff      1 2 0.0 1.0 0.5

delete_atoms    overlap 0.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 14 14 1
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command delete_atoms, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/2d
      bin: standard
  (2) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 12776 atoms, new total = 17353

# SRD run

reset_timestep  0

neighbor        0.3 multi
neigh_modify    delay 0 every 1 check yes

comm_modify     mode multi group big vel yes
neigh_modify    include big

# no pairwise interactions with small particles

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0
pair_coeff      2 2 0.0 1.0 0.0
pair_coeff      1 2 0.0 1.0 0.0

# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles

timestep        0.001

fix             1 big rigid molecule
  100 rigid bodies with 200 atoms
fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 collision slip inside ignore overlap yes
fix             3 all enforce2d

# diagnostics

compute         tbig big temp/sphere
variable        pebig equal pe*atoms/count(big)
variable        ebig equal etotal*atoms/count(big)
thermo_style    custom step temp f_2[8] etotal v_pebig v_ebig press                 f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]                 f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]

thermo_modify   temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo          1000

#dump           1 all atom 1000 dump.dimer

#dump           1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify    1 pad 6 adiam 1 1 adiam 2 0.2

run             10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2

@Article{Intveld08,
 author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
 title =   {Accurate and Efficient Methods for Modeling Colloidal
            Mixtures in an Explicit Solvent using Molecular Dynamics},
 journal = {Comput.\ Phys.\ Commut.},
 year =    2008,
 volume =  179,
 pages =   {320--329}
}

@article{Shire2020,
 author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
 title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
          Detection Applied to Investigate the Quasi-Static Limit},
 journal = {Computational Particle Mechanics},
 year = {2020}
@article{Monti2022,
 author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
           and Lechman, Jeremy B.},
 title = {Large-scale frictionless jamming with power-law particle 
          size distributions},
 journal = {Phys. Rev. E},
 volume = {106}
 issue = {3}
 year = {2022}
}

- fix srd command: doi:10.1063/1.3419070

@Article{Petersen10,
 author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
 G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
 title =   {Mesoscale Hydrodynamics via Stochastic Rotation
    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
 journal = {J.~Chem.\ Phys.},
 year =    2010,
 volume =  132,
 pages =   174106
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
  SRD/big particles = 17153 200
  big particle diameter max/min = 1 1
  SRD temperature & lamda = 1 0.063245553
  SRD max distance & max velocity = 0.25298221 12.649111
  SRD grid counts: 75 75 1
  SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
  SRD per actual grid cell = 5.544404
  SRD viscosity = 0.23553122
  big/SRD mass density ratio = 0.14250828
  # of rescaled SRD velocities = 0
  ave/max small velocity = 4.191188 7.6900178
  ave/max big velocity = 2.6813242 7.1846104
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 18.683304, bins = 1 1 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/multi/atomonly/newton
      stencil: half/multi/2d
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 26.77 | 26.77 | 26.77 Mbytes
   Step          Temp          f_2[8]         TotEng        v_pebig         v_ebig         Press          f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]         f_2[6]         f_2[7]         f_2[8]         f_2[9]        f_2[10]        f_2[11]        f_2[12]    
         0   6.8392143      0              0.297476       20.71529       25.810505      4.0555741      0              0              0              0              0              0              0              0              0              0              0              0            
      1000   1.2285566      3375           0.24673495     20.492683      21.407958      5.237464       13477          54             54             1              652            16900          5625           3375           1.1653557      0              15             0            
      2000   1.3561011      3395           0.24763991     20.476182      21.486477      9.2878509      13435          67             67             0              1504           16900          5625           3395           1.1651182      0              15             0            
      3000   1.2445369      3352           0.24713723     20.515681      21.442861      8.0289529      13186          62             63             2              2379           16900          5625           3352           1.1746721      0              15             0            
      4000   1.1058201      3389           0.24596239     20.51709       21.340926      10.003266      13466          66             66             0              3264           16900          5625           3389           1.1671415      0              15             0            
      5000   1.0584198      3407           0.24539623     20.503281      21.291804      9.1119405      13254          64             64             0              4189           16900          5625           3407           1.1687685      0              15             0            
      6000   1.3335611      3360           0.24737788     20.470239      21.463742      8.6885126      13281          62             62             1              5031           16900          5625           3360           1.1568996      0              15             0            
      7000   1.1384759      3401           0.24570869     20.47075       21.318914      9.1801119      13059          47             47             1              5878           16900          5625           3401           1.182474       0              15             0            
      8000   1.2982334      3397           0.24667224     20.435333      21.402517      6.5904007      13405          56             56             0              6729           16900          5625           3397           1.169017       0              24             0            
      9000   1.0456752      3381           0.24504517     20.482316      21.261344      10.497413      13205          81             81             2              7706           16900          5625           3381           1.1694675      0              24             0            
     10000   1.2222547      3394           0.24653264     20.479825      21.390405      8.7495888      13296          68             68             1              8581           16900          5625           3394           1.1613437      0              24             0            
Loop time of 7.18514 on 1 procs for 10000 steps with 17353 atoms

Performance: 120248.165 tau/day, 1391.761 timesteps/s, 24.151 Matom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.14497    | 0.14497    | 0.14497    |   0.0 |  2.02
Neigh   | 0.031835   | 0.031835   | 0.031835   |   0.0 |  0.44
Comm    | 0.094201   | 0.094201   | 0.094201   |   0.0 |  1.31
Output  | 0.00082765 | 0.00082765 | 0.00082765 |   0.0 |  0.01
Modify  | 6.8507     | 6.8507     | 6.8507     |   0.0 | 95.35
Other   |            | 0.06259    |            |       |  0.87

Nlocal:          17353 ave       17353 max       17353 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:            128 ave         128 max         128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:           1334 ave        1334 max        1334 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1334
Ave neighs/atom = 0.076874316
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:07
